First, let me clarify a few things. Pixel Sonic, Tails, and Dr. Egg an came from Sonic 2 and the characters are 4 years younger then. This is my theory on the timeline (shared by some people, but how I think it went).
Sonic's Story
It doesn't matter now what happens. I will never give up the fight! There is no way I will run away from all of my frights. Long as the voice inside me says go I will always keep on running. There is no way to stop me from going to the very top. It doesn't matter who is wrong or who is right.
Pixel Sonic and Pixel Tails came out of the portal from the future. Sonic told Tails, "Did you see how cool I wasn't? I knew I was fast, but not that fast." Tails responded, "Yeah, you're quite full of surprises."
Sonic started running into the jungle. "Where are you going?" "If I'm going to be as cool as my future self, I better start training." So Sonic ran through Green Hill Zone.
Every day he was running. He eventually managed to learn the homing attack he could use. But he still couldn't master the boost his future self could use. He could only do a limited version in mid air. It helped him cross larger gaps, but it was hard to perfect. It didn't matter. After seeing his future self, he was more confident than ever.
Many things happened over the next few years, Sonic noticed something that was strange. None of the adventures his future self mentioned actually happened.
What was going on?